rs60813083

Variant names:

• chr20-49962709-T-G
• rs60813083

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.091 in 152,082 control chromosomes in the GnomAD database, including 673 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.091 (673 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.118 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0910 AC: 13832 AN: 151966 Hom.: 675 Cov.: 31

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.0989

Gnomad AMR AF: 0.0676

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.0400

Gnomad SAS AF: 0.0930

Gnomad FIN AF: 0.0846

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0799

Gnomad OTH AF: 0.0939

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0910 AC: 13838 AN: 152082 Hom.: 673 Cov.: 31 AF XY: 0.0901 AC XY: 6700 AN XY: 74368

African (AFR) AF: 0.121 AC: 5018 AN: 41484

American (AMR) AF: 0.0674 AC: 1029 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.140 AC: 486 AN: 3464

East Asian (EAS) AF: 0.0397 AC: 205 AN: 5164

South Asian (SAS) AF: 0.0936 AC: 451 AN: 4820

European-Finnish (FIN) AF: 0.0846 AC: 897 AN: 10604

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.0800 AC: 5435 AN: 67974

Other (OTH) AF: 0.0934 AC: 197 AN: 2110

Alfa AF: 0.0860 Hom.: 64

Bravo AF: 0.0916

Asia WGS AF: 0.0610 AC: 211 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	8.1
DANN	Benign	0.77
PhyloP100		0.21

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs60813083; hg19: chr20-48579246;